Spirulina (Arthrospira) platensis is the most commonly produced microalgae for commercial applications, such as nutraceuticals and feed. While crop productivity of commercial Spirulina farms is often compromised by grazers and contaminating microzooplanktons, the biodiversity and identity of the most harmful microzooplanktons in Spirulina farms have not been extensively studied. As China is the number one producer of Spirulina in the world, comprehensive information on the biodiversity and identity of microzooplanktons in Spirulina farms is essential for the long-term commercial viability of these farms. Therefore, we determined the biodiversity and identity of the major microzooplanktons that are present in eight commercial Spirulina cultivation sites throughout China. Furthermore, we identified the major grazers that appear to directly affect the productivity of Spirulina cultures. Among twenty-three species that include 2 flagellates, 2 amoebae, 15 ciliates, and 4 rotifers, Brachionus plicatilis, Frontonia sp. and one unknown Heterolobosean amoeba appeared to be the most harmful to Spirulina due to their high density and ability to graze Spirulina. The similarity of the biodiversity and abundance of the microzooplankton was > 80% among two out of eight mass cultivation sites (C and D), while the remaining cultivation sites exhibited their own unique microzooplankton biodiversity characteristics. Redundancy analysis (RDA) showed that there was a positive relationship between harmful species of Brachionus plicatilis and salinity, while the other two harmful species of Heterolobosean amoeba and Frontonia sp. had a positive relationship with oxidation-reduction potential (ORP). As this is the first report to identify the major harmful microzooplankton species in commercial Spirulina farms, our study not only provides a theoretical basis for the relationship between environmental factors and biodiversity of harmful grazers but also lays a scientific foundation for developing effective monitoring and management strategies for commercial Spirulina farms.